Sage 9.5.beta5 released

Volker Braun

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Oct 29, 2021, 5:42:11 PM10/29/21

to sage-release

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

f716a0b366 (tag: 9.5.beta5, trac/develop) Updated SageMath version to 9.5.beta5

c5a87834e7 Trac #32758: fix E713 and E714 in schemes

50776daec4 Trac #32757: last fixes for relint linter

d95005e277 Trac #32756: fix E713 and E714 in combinat

60c6b1911d Trac #32755: fix E713 and E714 in rings

8a27526e7c Trac #32722: argcomplete should be a standard package

bac0d56c89 Trac #32660: Add sage.rings.abc.{AlgebraicField,...,NumberField_quadratic}, deprecate is_AlgebraicField, ..., is_CyclotomicField, is_QuadraticField

7dd78eff36 Trac #2877: security risk -- restrict the input of eval in CC constructor

cf1a7a533d Trac #32205: Removing deprecated parameters and methods in projective_ds

0574dae5f9 Trac #32635: sage.matrix.matrix_space: Import element classes on demand, fall back to generic on ImportError

61d9294bcd Trac #32743: use .pair() for quaternions instead of inlining the definition

bf65712f5f Trac #32739: change order of indices in doc test of quantum determinant

cd3aa6fbac Trac #32555: Typo in doc/en/developer/portability_testing.rst

72e76991cd Trac #32446: fix doctest formatting in schemes/elliptic_curves/ell_curve_isogeny.py

363c071d57 Trac #32632: computing elliptic-curve isomorphisms in characteristic 2 sometimes fails

9fdf3832f9 Trac #32630: Fix docstring in Polyhedron method representative_point

a15c58c9d6 Trac #32582: Add colored Jones polynomial

f35c2c81c3 Trac #17442: Italian translation of tutorial

c1a55a62d1 Trac #32729: working on annotations in combinat

37afc35b18 Trac #32728: Get rid of <type in doctests and the mechanism that allows this

d8e6aed16d Trac #32717: Move sage.functions.other.sqrt to sage.misc.functional

5ddfc23e0a Trac #32695: 5 internet doctests failing in src/sage/databases/oeis.py

753406109a Trac #32656: Eliminate psutil (memory management) dependency

04a39c6e1b Trac #29024: spkg-configure.m4 for singular

8ba7c02710 Trac #28207: Derivative of piecewise function returns junk

b970bc92d1 Trac #32737: Fix doctest in src/sage/rings/integer.pyx

ec536c7872 Trac #32495: EllipticCurveIsogeny._richcmp_ does not use the kernel polynomial

9750b0ef92 Trac #32490: multiplication_by_m_isogeny is only correct up to automorphism

b6b1b25e77 Trac #32469: Improve ecl interface

7407db130b Trac #32445: Do not access M4RI internals

5e674821ad Trac #32440: shifting power series doesn't keep track of precision correctly

bc6791f518 Trac #32430: remove obsolete code in EllipticCurveIsogeny.is_normalized()

225ac125f8 Trac #32723: Helper function to avoid duplicated code when using weights

1a9bb6d29d Trac #32680: more pycodestyle checks again

3c6a07afc9 Trac #32727: complete mpir deletion

56ec53a51b Trac #32712: sage.tensor.modules: make doctests involving SR optional

11684c278f Trac #32708: sage.tensor.modules: remove dependency on sage.manifolds

a8e7da2709 Trac #32691: setuptools: Upgrade to 58.2.0, remove old easy_install patch

4e42232b97 Trac #32690: add factor method to interval-posets

e87eb57a8e Trac #32685: Ill-placed y label in sage.manifolds.utilities.set_axes_labels

20e5ed68cc Trac #32684: various details in combinat and functions

e75948b94e Trac #32637: Add sage.geometry.abc; remove uses of is_Polyhedron, is_LatticePolytope, is_Cone outside of sage.geometry

08d189cd3a Trac #32607: compatibility with gsl 2.7

fa012254ac Trac #32665: Deprecate is_[Callable]SymbolicExpressionRing, remove use of is_Symbolic{Equation,Variable}, is_CallableSymbolicExpression

e7f6b13107 Trac #32649: Replace sage.doctest.external.has_* functions by Features

aac663be0d Trac #32659: sdh_pip_install: Force reinstallation of built wheels; add sage_setup source deps

056b8d4e7b (tag: 9.5.beta4) Updated SageMath version to 9.5.beta4

William Stein

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Oct 29, 2021, 7:39:56 PM10/29/21

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Hi,

I tried building on a pretty clean Macbook Pro M1 with the new MacOS 12.0.1 Montery, and it didn't get very far, failing pretty quickly on GMP. For what it is worth, I had no trouble building GMP directly on this computer (nothing to do with Sage).

-- William

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--

William (http://wstein.org)

config.log

gmp-6.2.0.log

install.log

Dima Pasechnik

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Oct 30, 2021, 3:19:32 AM10/30/21

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On Sat, 30 Oct 2021, 01:39 William Stein, <wst...@gmail.com> wrote:

Hi,

I tried building on a pretty clean Macbook Pro M1 with the new MacOS 12.0.1 Montery, and it didn't get very far, failing pretty quickly on GMP. For what it is worth, I had no trouble building GMP directly on this computer (nothing to do with Sage).

is it because we are still on GMP 6.2.0 ?

(GMP current is 6.2.1)

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CACLE5GB2%2Bor%3D_qXN53TKFTazondH%3DX_jA45YU6wooMa%2B%3D2AGkA%40mail.gmail.com.

Dima Pasechnik

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Oct 30, 2021, 3:49:02 AM10/30/21

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please see https://trac.sagemath.org/ticket/32796 (upgrade to gmp 6.2.1)

Emmanuel Charpentier

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Oct 30, 2021, 8:40:35 AM10/30/21

to sage-release

I tried to upgrade 9.5.beta3 to 9.5.beta5 ith the following packages installed :

cmdstanpy...............................? (0.9.77)
cypari2.................................? (2.1.2)
dot2tex.................................2.11.3.p0 (2.11.3.p0)
fricas..................................1.3.7.p1 (1.3.7.p1)
gap_packages............................4.11.1 (4.11.1)
json5...................................? (0.9.6)
jupyterlab..............................3.2.1 (2.2.10)
jupyterlab_server.......................? (1.2.0)
jupyterlab_widgets......................none (2.0)
libsemigroups...........................1.1.0 (1.1.0)
nodeenv.................................1.6.0 (1.4.0)
nodejs..................................none (12.18.3)
nose....................................? (1.3.7)
pandas..................................? (1.3.3)
psutil..................................? (5.2.0.p2)
python_dateutil.........................? (2.8.1)
sagemath_standard.......................? (9.5b5)
ujson...................................? (4.2.0)

ptestlong gives the following looong list of failures crashing Sage :

sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/elliptic_curves/isogeny_small_degree.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/elliptic_curves/ell_rational_field.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/elliptic_curves/ell_number_field.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/cyclic_covers/cycliccover_finite_field.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/pollack_stevens/modsym.py  # 9 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/number_field/number_field.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform/element.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/dynamics/arithmetic_dynamics/projective_ds.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/graphs/generic_graph.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform/ring.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/elliptic_curves/heegner.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/interfaces/fricas.py  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/btquotients/pautomorphicform.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/misc/sageinspect.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix_integer_dense_hnf.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/local_comp/local_comp.py  # 4 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform_hecketriangle/hecke_triangle_group_element.py  # 8 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modules/free_module_integer.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/elliptic_curves/ell_curve_isogeny.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform_hecketriangle/graded_ring_element.py  # 25 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/arith/misc.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/qqbar.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform_hecketriangle/readme.py  # 12 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix2.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/combinat/tutorial.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/quadratic_forms/genera/genus.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/calculus/calculus.py  # 5 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform_hecketriangle/abstract_space.py  # 21 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/combinat/partition.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/abvar/abvar.py  # 10 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform/ambient_R.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix_integer_dense.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/misc/cachefunc.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/algebras/quatalg/quaternion_algebra.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform/constructor.py  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modules/free_quadratic_module_integer_symmetric.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/birds_other.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/abvar/lseries.py  # 8 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modsym/space.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/benchmark.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/btquotients/btquotient.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/number_field/S_unit_solver.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/overconvergent/genus0.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/hecke/submodule.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/typeset/ascii_art.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform_hecketriangle/element.py  # 10 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/functions/log.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/schemes/plane_conics/con_rational_function_field.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/structure/sage_object.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix_rational_dense.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/ipython_extension.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/interpreter.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/hecke/module.py  # 2 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/number_field/order.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modules/fg_pid/fgp_module.py  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/ja/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/combinat/quickref.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/fr/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/tr/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/pt/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/de/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/graphs/base/static_sparse_graph.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/hu/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/it/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/en/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix_cyclo_dense.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/es/a_tour_of_sage/index.rst  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/combinat/combinat.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/functions/transcendental.py  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/matrix_integer_sparse.pyx  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modsym/subspace.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/hecke/element.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modsym/tests.py  # 1 doctest failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/display/formatter.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/interface_magic.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/modabvar.rst  # 3 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/tests/book_stein_modform.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/ipython_tests.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/attach.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/abvar/cuspidal_subgroup.py  # 9 doctests failed
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/polynomial/real_roots.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/quadratic_forms/quadratic_form__local_density_interfaces.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/constructor.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/modform/vm_basis.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/bernmm.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/repl/rich_output/backend_ipython.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/modular/buzzard.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/interfaces/macaulay2.py  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/libs/flint/arith.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/matrix/misc.pyx  # Killed due to segmentation fault
sage -t --long --warn-long 215.7 --random-seed=276876733579103606015550424535934104048 src/sage/rings/bernoulli_mod_p.pyx  # Killed due to segmentation fault

Python error messages seen (but not logged) during ptestlong or attempts to reproduce the tests point to a problem in cypari2 which somehow managed to invite itself.

I’ll try to recompile after distclean, reinstall packages (cautiously avoiding cypari2), retest and report.

HTH,

Samuel Lelièvre

unread,

Oct 30, 2021, 9:09:41 AM10/30/21

to sage-release

2021-10-29 21:42 UTC, Volker Braun:
>
> f716a0b366 (tag: 9.5.beta5) Updated SageMath version to 9.5.beta5

Thanks for this new release!

On Debian 10 buster, `make -s V=0 ptestlong` resulted in
doctest failures in two files, after a successful build.

The files which had doctest failures are:
- src/sage/schemes/toric/sheaf/klyachko.py
failure tracked at #32773
- src/sage/interfaces/fricas.py
not sure that doctest failure is tracked yet

Details below.

-----

```
$ ./bootstrap -q && ./configure -q && make -s V=0 ptestlong
...
----------------------------------------------------------------------
sage -t --long --random-seed=229468210681390191126905811150024665118
src/sage/schemes/toric/sheaf/klyachko.py # 1 doctest failed
sage -t --long --random-seed=229468210681390191126905811150024665118

src/sage/interfaces/fricas.py # 1 doctest failed

----------------------------------------------------------------------
...
```

```
$ SEED=229468210681390191126905811150024665118
$ alias sage-test="./sage -t --long --random-seed=${SEED}"
```

```
$ sage-test src/sage/schemes/toric/sheaf/klyachko.py

too many failed tests, not using stored timings
Running doctests with ID 2021-10-29-14-40-23-34a510a8.
Git branch: develop
Using --optional=build,ccache,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,pip,pysingular,saclib,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg
Doctesting 1 file.
sage -t --long --random-seed=229468210681390191126905811150024665118
src/sage/schemes/toric/sheaf/klyachko.py
**********************************************************************
File "src/sage/schemes/toric/sheaf/klyachko.py", line 950, in
sage.schemes.toric.sheaf.klyachko.KlyachkoBundle_class.random_deformation
Failed example:
Vtilde.cohomology(dim=True, weight=(0,))
Expected:
(1, 0)
Got:
(0, 0)
**********************************************************************
1 item had failures:
1 of 7 in sage.schemes.toric.sheaf.klyachko.KlyachkoBundle_class.random_deformation
[151 tests, 1 failure, 10.63 s]
----------------------------------------------------------------------
sage -t --long --random-seed=229468210681390191126905811150024665118
src/sage/schemes/toric/sheaf/klyachko.py # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 10.9 seconds
cpu time: 9.8 seconds
cumulative wall time: 10.6 seconds
Pytest is not installed, skip checking tests that rely on it.
```

```
$ sage-test src/sage/interfaces/fricas.py

too many failed tests, not using stored timings
Running doctests with ID 2021-10-29-14-41-48-fefac262.
Git branch: develop
Using --optional=build,ccache,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,pip,pysingular,saclib,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg
Doctesting 1 file.
sage -t --long --random-seed=229468210681390191126905811150024665118
src/sage/interfaces/fricas.py
**********************************************************************
File "src/sage/interfaces/fricas.py", line 1193, in
sage.interfaces.fricas.FriCASElement._latex_
Failed example:
latex(fricas("integrate(sin(x+1/x),x)")) #
optional - fricas
Expected:
\int ^{\displaystyle x} {{\sin \left( {{{{{ \%O} ^{2}}+1} \over
\%O}} \right)} \ {d \%O}}
Got:
\int ^{\displaystyle x} {{\sin \left( {{{{{ \%A} ^{2}}+1} \over
\%A}} \right)} \ {d \%A}}
**********************************************************************
1 item had failures:
1 of 4 in sage.interfaces.fricas.FriCASElement._latex_
[277 tests, 1 failure, 45.49 s]
----------------------------------------------------------------------
sage -t --long --random-seed=229468210681390191126905811150024665118

src/sage/interfaces/fricas.py # 1 doctest failed

----------------------------------------------------------------------
Total time for all tests: 50.6 seconds
cpu time: 6.9 seconds
cumulative wall time: 45.5 seconds
Pytest is not installed, skip checking tests that rely on it.
```

Emmanuel Charpentier

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Oct 30, 2021, 11:55:30 AM10/30/21

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Aaaarghhh : cypari2 is installed by Sage itself : after (some operations amounting to removing Python packages, then) make distclean && make :

charpent@zen-book-flip:/usr/local/sage-9$ sage -optional | grep -v ot_instal
/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/misc/package.py:116: UserWarning: failed to fetch the version of pkg='ore_algebra' at https://pypi.org/pypi/ore_algebra/json
  warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url))
[package]...............................[latest version] ([version])

cypari2.................................? (2.1.2)
python_dateutil.........................? (2.8.1)
sagemath_standard.......................? (9.5b5)

I’ll reinstall the other packages and retest notwithstanding…

Emmanuel Charpentier

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Oct 30, 2021, 2:34:21 PM10/30/21

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After rebuilding and reinstalling the same (really) optional packages, `ptestlong` gets exactly one (reproducible) failure, i. e. the one reported by Samuel Lelièvre.

I am at loss as to why I needed to rebuild 9.5 from sratch instead of upgrading from 9.3. Ideas ?

HTH,

Samuel Lelievre

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Oct 30, 2021, 5:54:43 PM10/30/21

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2021-10-30 18:34:21 UTC, Emmanuel Charpentier:

>

> After rebuilding and reinstalling the same (really)

> optional packages, `ptestlong` gets exactly one

> (reproducible) failure, i. e. the one reported by

> Samuel Lelièvre.
>
> I am at loss as to why I needed to rebuild 9.5

> from sratch instead of upgrading from 9.3. Ideas?

I'm sure you mean: "why I needed to rebuild 9.5.beta5

from scratch instead of upgrading from 9.5.beta3".

Not sure why a distclean was needed in that case.

William Stein

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Nov 1, 2021, 6:18:21 PM11/1/21

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I tried to build sage-9.5.beta5 on a very clean Linux Ubuntu:20.04 image with standard dev packages (in Docker) but on an ARM aarch64 architecture instead of Intel. It fails with Tachyon simply saying "Error: Sorry, your platform isn't supported by Tachyon and/or Sage. Exiting...". I don't know what that is about.

I found https://trac.sagemath.org/ticket/23712 which is a 2-year old ticket about how upgrading Tachyon is needed " to make Sage work on arm64/aarch64."

Any suggestions? My goal is to make an aarch64 version of the cocalc-docker image. Is there an easy workaround for this problem, or should I just do some hack to disable building tachyon (since it is a runtime only dependency)? Is the right way to disable building a standard package these days still to touch some file somewhere, or did that change?

gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)
****************************************************
Package 'tachyon' is currently not installed
No legacy uninstaller found for 'tachyon'; nothing to do
****************************************************************************************
Error: Sorry, your platform isn't supported by Tachyon and/or Sage. Exiting...
****************************************************************************************

real 0m0.013s
user 0m0.007s
sys 0m0.009s
************************************************************************
Error installing package tachyon-0.98.9.p7
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log files
/usr/local/sage/logs/pkgs/tachyon-0.98.9.p7.log
and
/usr/local/sage/config.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage/local/var/tmp/sage/build/tachyon-0.98.9.p7 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage/local/var/tmp/sage/build/tachyon-0.98.9.p7' && '/usr/local/sage/sage' --buildsh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

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William (http://wstein.org)

Isuru Fernando

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Nov 1, 2021, 6:27:18 PM11/1/21

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Hi William,

tachyon and sage work just fine on conda where we have an aarch64 build.

We use the `linux-64-thr` option for aarch64.

See https://github.com/sagemath/sage/blob/a89f81d7783df2d4e4a187bf209e94d128301f83/build/pkgs/tachyon/spkg-install.in#L19-L36

Isuru

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Dima Pasechnik

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Nov 1, 2021, 6:37:42 PM11/1/21

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On Mon, Nov 1, 2021 at 10:18 PM William Stein <wst...@gmail.com> wrote:

I tried to build sage-9.5.beta5 on a very clean Linux Ubuntu:20.04 image with standard dev packages (in Docker) but on an ARM aarch64 architecture instead of Intel. It fails with Tachyon simply saying "Error: Sorry, your platform isn't supported by Tachyon and/or Sage. Exiting...". I don't know what that is about.

I found https://trac.sagemath.org/ticket/23712 which is a 2-year old ticket about how upgrading Tachyon is needed " to make Sage work on arm64/aarch64."

Any suggestions? My goal is to make an aarch64 version of the cocalc-docker image. Is there an easy workaround for this problem, or should I just do some hack to disable building tachyon (since it is a runtime only dependency)? Is the right way to disable building a standard package these days still to touch some file somewhere, or did that change?

Just install the system tachyon package, and let ./configure do its job.

You don't need to build it.

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William Stein

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Nov 1, 2021, 7:28:44 PM11/1/21

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Great idea. Thanks Dima!

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq3FDgxH_UOcEhMY1wvbLkvEPkMhjchtPMDJ1X6YzG7DmQ%40mail.gmail.com.

--

William (http://wstein.org)

Dima Pasechnik

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Nov 1, 2021, 7:35:36 PM11/1/21

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On Mon, Nov 1, 2021 at 11:28 PM William Stein <wst...@gmail.com> wrote:

Great idea. Thanks Dima!

On Mon, Nov 1, 2021 at 3:37 PM Dima Pasechnik <dim...@gmail.com> wrote:

On Mon, Nov 1, 2021 at 10:18 PM William Stein <wst...@gmail.com> wrote:
I tried to build sage-9.5.beta5 on a very clean Linux Ubuntu:20.04 image with standard dev packages (in Docker) but on an ARM aarch64 architecture instead of Intel. It fails with Tachyon simply saying "Error: Sorry, your platform isn't supported by Tachyon and/or Sage. Exiting...". I don't know what that is about.
I found https://trac.sagemath.org/ticket/23712 which is a 2-year old ticket about how upgrading Tachyon is needed " to make Sage work on arm64/aarch64."

Any suggestions? My goal is to make an aarch64 version of the cocalc-docker image. Is there an easy workaround for this problem, or should I just do some hack to disable building tachyon (since it is a runtime only dependency)? Is the right way to disable building a standard package these days still to touch some file somewhere, or did that change?

by the way, it would be great to know if our usual "install as many system packages as ./configure advises

at the end" scheme works well on aarch64, don't stop at tachyon please.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CACLE5GAHQpnqrfC74jimwXA-UXU4j%2BLSE98tvW2%3DyMQ%2BC05okw%40mail.gmail.com.

William Stein

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Nov 1, 2021, 8:33:40 PM11/1/21

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On Mon, Nov 1, 2021 at 4:35 PM Dima Pasechnik <dim...@gmail.com> wrote:

On Mon, Nov 1, 2021 at 11:28 PM William Stein <wst...@gmail.com> wrote:
Great idea. Thanks Dima!

On Mon, Nov 1, 2021 at 3:37 PM Dima Pasechnik <dim...@gmail.com> wrote:

On Mon, Nov 1, 2021 at 10:18 PM William Stein <wst...@gmail.com> wrote:
I tried to build sage-9.5.beta5 on a very clean Linux Ubuntu:20.04 image with standard dev packages (in Docker) but on an ARM aarch64 architecture instead of Intel. It fails with Tachyon simply saying "Error: Sorry, your platform isn't supported by Tachyon and/or Sage. Exiting...". I don't know what that is about.
I found https://trac.sagemath.org/ticket/23712 which is a 2-year old ticket about how upgrading Tachyon is needed " to make Sage work on arm64/aarch64."

Any suggestions? My goal is to make an aarch64 version of the cocalc-docker image. Is there an easy workaround for this problem, or should I just do some hack to disable building tachyon (since it is a runtime only dependency)? Is the right way to disable building a standard package these days still to touch some file somewhere, or did that change?

by the way, it would be great to know if our usual "install as many system packages as ./configure advises
at the end" scheme works well on aarch64, don't stop at tachyon please.

Good idea, definitely.

Is there an official Dockerfile for building Sage these days somewhere? I'm using one that I found years ago from @ebray, and all that advertisement about the fantastic support for system-wide packages (which I forgot about) is hidden behind automation. [searches...]. Yes, there is:

https://github.com/sagemath/sage/blob/develop/docker/Dockerfile

That's a pretty enormous Dockerfile, and I imagine it solves many subtle problems. A cursory glance suggests that it installs a minimal collection of system-wide packages. Maybe somebody should try what you just suggested (modify it to depend on system packages) starting with that Dockerfile too, to see how it goes (or as a different CI test)...

William

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--

William (http://wstein.org)

William Stein

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Nov 2, 2021, 12:13:25 PM11/2/21

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This is a quick update about building the 9.5.beta5 version of Sage on an M1 Mac under Docker aarch64 Linux.

After installing Tachyon system wide, the build completes. This Cython module won't import due to an issue with libgomp, which

is evidently some openMP parallel computing library, failing with " /lib/aarch64-linux-gnu/libgomp.so.1: cannot allocate memory in static TLS block".

See below for the failed test.

A quick search reveals this discussion of exactly this sort of problem:

https://github.com/opencv/opencv/issues/14884

It sounds like a bug in how SageMath is built (or the library is imported) that will need a workaround on aarch64. This comment

https://github.com/opencv/opencv/issues/14884#issuecomment-815632861

seems most actionable.

I was NOT able to reproduce this by just starting sage or Python and importing modules. It has something to

do with how doctests are run.

The suggestion in the github issue I link to above to use LD_PRELOAD *does* work, i.e.,

LD_PRELOAD=/lib/aarch64-linux-gnu/libgomp.so.1 ./sage -t src/sage/algebras/quatalg/quaternion_algebra_cython.pyx

...

works fine. I might just set LD_PRELOAD for cocalc-docker if nobody has a better idea. I'm keeping track of all these

issues with Sage + aarch64 here: https://github.com/sagemathinc/cocalc-docker/issues/138

---

root@8bff70fbbc1c:/usr/local/sage# ./sage -t src/sage/algebras/quatalg/quaternion_algebra_cython.pyx
no stored timings available
Running doctests with ID 2021-11-02-15-54-57-8a128eb1.
Git branch: HEAD
Using --optional=build,debian,dochtml,pip,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg
Doctesting 1 file.
Traceback (most recent call last):
File "/usr/local/sage/src/bin/sage-runtests", line 151, in <module>
err = DC.run()
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", line 1254, in run
self.run_doctests()
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", line 951, in run_doctests
self.dispatcher = DocTestDispatcher(self)
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/forker.py", line 1614, in __init__
init_sage(controller)
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/forker.py", line 192, in init_sage
controller.load_environment()
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", line 572, in load_environment
return import_module(self.options.environment)
File "/usr/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 848, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/repl/ipython_kernel/all_jupyter.py", line 5, in <module>
from sage.all_cmdline import *
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/all_cmdline.py", line 19, in <module>
from sage.all import *
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/all.py", line 129, in <module>
from sage.algebras.all import *
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/all.py", line 21, in <module>
import sage.algebras.catalog as algebras
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/catalog.py", line 80, in <module>
from sage.algebras.quatalg.quaternion_algebra import QuaternionAlgebra as Quaternion
File "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/quatalg/quaternion_algebra.py", line 69, in <module>
from . import quaternion_algebra_cython
File "sage/algebras/quatalg/quaternion_algebra_cython.pyx", line 1, in init sage.algebras.quatalg.quaternion_algebra_cython (build/cythonized/sage/algebras/quatalg/quaternion_algebra_cython.cpp:6215)
File "sage/matrix/matrix_integer_dense.pyx", line 1, in init sage.matrix.matrix_integer_dense (build/cythonized/sage/matrix/matrix_integer_dense.cpp:57704)
ImportError: /lib/aarch64-linux-gnu/libgomp.so.1: cannot allocate memory in static TLS block

--

William (http://wstein.org)

Matthias Köppe

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Nov 2, 2021, 1:21:17 PM11/2/21

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On Tuesday, November 2, 2021 at 9:13:25 AM UTC-7 William Stein wrote:

This is a quick update about building the 9.5.beta5 version of Sage on an M1 Mac under Docker aarch64 Linux.

A quick remark: Sage developers who want to help on this issue do not need this specific hardware.

Using macOS Docker Desktop, the following command runs a build of Sage in this architecture. (It's slow because it involves CPU emulation.)

$ tox -e docker-ubuntu-groovy-standard-arm64v8

William didn't say which distribution he is working with; see SAGE_ROOT/tox.ini for the distributions that our portability testing scripts support.

William Stein

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Nov 2, 2021, 1:32:20 PM11/2/21

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Thanks. I'm using ubuntu:20.04. It's this Dockerfile -- https://github.com/sagemathinc/cocalc-docker/blob/master/Dockerfile -- but with an apt-get to install tachyon, and replacing "9.2" with "9.5.beta5" in the build of Sage.

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William Stein

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Nov 2, 2021, 1:56:29 PM11/2/21

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Here's how "make test" ended:

sage -t --random-seed=225297532770316936918573996029610176361 src/sage/groups/class_function.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/groups/perm_gps/symgp_conjugacy_class.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/groups/perm_gps/permgroup.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/coding/binary_code.pyx # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/coding/linear_code.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/dynamics/arithmetic_dynamics/projective_ds.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/interfaces/singular.py # 3 doctests failed
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/rings/qqbar.py # Timed out
sage -t --random-seed=225297532770316936918573996029610176361 src/sage/tests/cmdline.py # 3 doctests failed
----------------------------------------------------------------------

The failures with singular are also timeouts -- I just saw Singular stuck at 0 percent for a long time and manually killed it.

So it looks like nothing is giving wrong answers, but a couple of things are randomly hanging.

-- William

--

William (http://wstein.org)

William Stein

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Nov 2, 2021, 2:03:17 PM11/2/21

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I just want to add that I don't trust Docker desktop on M1 yet, and it could easily be responsible for these problems.

E.g., I've found that often wget sometimes segfaults in this exact container, and that has nothing to do with Sage.

Does anybody do test builds of Sage on other aarch64 linux platforms, e.g., recent Rasberry Pi?

--

William (http://wstein.org)

Dima Pasechnik

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Nov 2, 2021, 2:48:19 PM11/2/21

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On Tue, Nov 2, 2021 at 6:03 PM William Stein <wst...@gmail.com> wrote:

I just want to add that I don't trust Docker desktop on M1 yet, and it could easily be responsible for these problems.
E.g., I've found that often wget sometimes segfaults in this exact container, and that has nothing to do with Sage.

Does anybody do test builds of Sage on other aarch64 linux platforms, e.g., recent Rasberry Pi?

RPi own OS is still 32-bit. I do have an RPi 4 in capboard, I wasn't able to find a way to create a working

64-bit installation media which doesn't need a physical monitor and keyboard

(should try in the office, I guess)

Dima

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Matthias Köppe

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Nov 2, 2021, 11:02:56 PM11/2/21

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I just built for this architecture successfully using "tox -e docker-ubuntu-groovy-standard-arm64v8" (on my Intel MBP). That's slightly newer than ubuntu-focal (20.04)

sage -t --random-seed=0 src/sage/algebras/quatalg/quaternion_algebra_cython.pyx
[10 tests, 0.17 s]

----------------------------------------------------------------------

All tests passed!

On Tuesday, November 2, 2021 at 9:13:25 AM UTC-7 William Stein wrote:

William Stein

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Nov 2, 2021, 11:37:54 PM11/2/21

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What did you do exactly? For example did you install tachyon systemwide?

Thanks!

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/9497b1ce-756a-4605-973a-cc577ea65355n%40googlegroups.com.

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-- William Stein

Matthias Köppe

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Nov 2, 2021, 11:59:58 PM11/2/21

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It's really just the command "tox -e docker-ubuntu-groovy-standard-arm64v8" - try it

William Stein

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Nov 3, 2021, 1:13:14 AM11/3/21

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On Tue, Nov 2, 2021 at 9:00 PM Matthias Köppe <matthia...@gmail.com> wrote:

It's really just the command "tox -e docker-ubuntu-groovy-standard-arm64v8" - try it

Thanks. Some more details I figured out in a few moments, in case anybody else is interested:

1. What is tox? Answer: it is a Python package you can install by typing "pip3 install tox". The homepage is https://tox.wiki/en/latest/, which explains that it is a test automation system.

2. How do you use it? Answer: Get the Sage source code and from the top level type "tox -e docker-ubuntu-groovy-standard-arm64v8".

This uses the file tox.ini that is in the top of the Sage source tree.

3. What is tox.ini? Where does it come from? Answer: Matthias added it to Sage a year ago. I don't know how it gets generated, but it seems very comprehensive.

4. Does it install tachyon from Ubuntu packages? Answer: I don't know, though "grep -i tachyon tox.ini" doesn't output anything, so I'm guessing it doesn't.

William

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/40ae90a8-e48a-40a7-81d5-6d9f37a5a557n%40googlegroups.com.

--

William (http://wstein.org)

Jaap Spies

unread,

Nov 3, 2021, 8:58:21 AM11/3/21

to sage-release

Hi William,

I'm using a Raspberry Pi 8GB with Raspberry OS 64 bit:

[dochtml] [thematic_] dumping search index in English (code: en)... done

[dochtml] [thematic_] The HTML pages are in local/share/doc/sage/html/en/thematic_tutorials.

[dochtml] Build finished. The built documents can be found in /home/pi/sagemath/sage-9.5.beta5/local/share/doc/sage/html/en/thematic_tutorials

make[2]: Leaving directory '/home/pi/sagemath/sage-9.5.beta5/build/make'

real 338m59.187s

user 1070m56.769s

sys 77m54.549s

Sage build/upgrade complete!

make[1]: Leaving directory '/home/pi/sagemath/sage-9.5.beta5'

pi@rasp8G64bit:~/sagemath/sage-9.5.beta5 $

make ptestlong:

----------------------------------------------------------------------

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/calculus/riemann.pyx # Killed due to segmentation fault

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/graphs/generic_graph.py # 1 doctest failed

----------------------------------------------------------------------

Total time for all tests: 21550.7 seconds

cpu time: 62314.9 seconds

cumulative wall time: 81945.2 seconds

Pytest is not installed, skip checking tests that rely on it.

make: *** [Makefile:202: ptestlong] Error 17

pi@rasp8G64bit:~/sagemath/sage-9.5.beta5 $

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/graphs/generic_graph.py

**********************************************************************

File "src/sage/graphs/generic_graph.py", line 577, in sage.graphs.generic_graph.GenericGraph.__eq__

Failed example:

G == H # most often true

Expected:

True

Got:

False

**********************************************************************

1 item had failures:

1 of 30 in sage.graphs.generic_graph.GenericGraph.__eq__

[3626 tests, 1 failure, 161.92 s]

----------------------------------------------------------------------

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/graphs/generic_graph.py # 1 doctest failed

----------------------------------------------------------------------

Total time for all tests: 165.2 seconds

cpu time: 117.8 seconds

cumulative wall time: 161.9 seconds

Pytest is not installed, skip checking tests that rely on it.

pi@rasp8G64bit:~/sagemath/sage-9.5.beta5 $ ./sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/calculus/riemann.pyx

Running doctests with ID 2021-11-03-13-29-10-d9382240.

Git branch: develop

Using --optional=build,debian,dochtml,pip,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg

Doctesting 1 file.

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/calculus/riemann.pyx

Unhandled SIGSEGV: A segmentation fault occurred.

This probably occurred because a *compiled* module has a bug

in it and is not properly wrapped with sig_on(), sig_off().

Python will now terminate.

------------------------------------------------------------------------

**********************************************************************

----------------------------------------------------------------------

sage -t --long --warn-long 370.6 --random-seed=127413209833813451099921915592124341248 src/sage/calculus/riemann.pyx # Killed due to segmentation fault

----------------------------------------------------------------------

Total time for all tests: 204.2 seconds

cpu time: 0.0 seconds

cumulative wall time: 0.0 seconds

Pytest is not installed, skip checking tests that rely on it.

pi@rasp8G64bit:~/sagemath/sage-9.5.beta5 $

Jaap

Matthias Köppe

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Nov 3, 2021, 12:30:31 PM11/3/21

to sage-release

On Tuesday, November 2, 2021 at 10:13:14 PM UTC-7 William Stein wrote:

On Tue, Nov 2, 2021 at 9:00 PM Matthias Köppe <matthia...@gmail.com> wrote:
It's really just the command "tox -e docker-ubuntu-groovy-standard-arm64v8" - try it

Thanks. Some more details I figured out in a few moments, in case anybody else is interested:

1. What is tox? Answer: it is a Python package you can install by typing "pip3 install tox". The homepage is https://tox.wiki/en/latest/, which explains that it is a test automation system.

2. How do you use it? Answer: Get the Sage source code and from the top level type "tox -e docker-ubuntu-groovy-standard-arm64v8".
This uses the file tox.ini that is in the top of the Sage source tree.

3. What is tox.ini? Where does it come from? Answer: Matthias added it to Sage a year ago. I don't know how it gets generated, but it seems very comprehensive.

tox.ini is not generated; it is source code, I wrote it.

You can read about it in:

https://doc.sagemath.org/html/en/developer/portability_testing.html

William Stein

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Nov 3, 2021, 1:09:25 PM11/3/21

to sage-release

Thanks!!!

--

William (http://wstein.org)

Sébastien Labbé

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Nov 4, 2021, 10:54:10 AM11/4/21

to sage-release

On Ubuntu 18.04 with few optional and external packages, I get:

Using --optional=4ti2,build,ccache,cryptominisat,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_numerical_backends_coin,sage_spkg

----------------------------------------------------------------------

sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/combinat/designs/incidence_structures.py # 1 doctest failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/databases/findstat.py # 9 doctests failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/dynamics/arithmetic_dynamics/projective_ds.py # 1 doctest failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/finance/stock.py # 1 doctest failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/graphs/generic_graph.py # 2 doctests failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/graphs/graph.py # 3 doctests failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/interfaces/fricas.py # 1 doctest failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/sat/solvers/dimacs.py # 2 doctests failed
sage -t --long --random-seed=170457515151866577504556719043729955415 src/sage/tests/cmdline.py # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc

These failures are already listed in:

https://trac.sagemath.org/ticket/25536

John Cremona

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Nov 4, 2021, 11:02:32 AM11/4/21

to sage-r...@googlegroups.com

I upgraded from a previous beta and there were no problems with make,
just two failures with make ptestlong:
sage -t --long --warn-long 133.0
--random-seed=133126240855796926255098246501347092842
src/sage/tests/cmdline.py # 3 doctests failed
sage -t --long --warn-long 133.0
--random-seed=133126240855796926255098246501347092842

src/sage/dynamics/arithmetic_dynamics/projective_ds.py # 1 doctest
failed

From the log file:

sage -t --long --warn-long 106.3 --random-seed=0 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 587, in
sage.tests.cmdline.test_executable
Failed example:
out.startswith("3.")

Expected:
True
Got:
False
**********************************************************************

File "src/sage/tests/cmdline.py", line 589, in
sage.tests.cmdline.test_executable
Failed example:
err
Expected:
''
Got:
'/home/john/sage/src/bin/sage: line 669: exec: sqlite3: not found\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 591, in
sage.tests.cmdline.test_executable
Failed example:
ret
Expected:
0
Got:
127

and

sage -t --long --warn-long 133.0
--random-seed=133126240855796926255098246501347092842
src/sage/dynamics/arithmetic_dynamics/projective_ds.py
**********************************************************************
File "src/sage/dynamics/arithmetic_dynamics/projective_ds.py", line
6943, in sage.dynamics.arithmetic_dynamics.projective_ds.?.conjugating_set
Failed example:
D6.conjugating_set(D6)
Expected:
[
[1 0] [0 1] [0 2] [4 0] [2 0] [0 4]
[0 1], [1 0], [1 0], [0 1], [0 1], [1 0]
]
Got:
[
[4 0] [2 0] [0 4] [1 0] [0 1] [0 2]
[0 1], [0 1], [1 0], [0 1], [1 0], [1 0]
]

In the second case it looks to me as if it is only that the list has
the same matrices in a different order.

Ubuntu 20.04.3 LTS, more details on request.

John

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Dima Pasechnik

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Nov 4, 2021, 11:16:09 AM11/4/21

to sage-release

failed test in

src/sage/tests/cmdline.py

indicates you need squlite binary installed, not only library.

this is an old bug in squlite spkg-configure, I thought it was fixed.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAD0p0K4hR%2BXA3nfVjk1Ew3w9RH%2BY7KkVZ-c1gxTY2oVip1QO_Q%40mail.gmail.com.

Sébastien Labbé

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Nov 4, 2021, 11:30:11 AM11/4/21

to sage-release

In the second case it looks to me as if it is only that the list has
the same matrices in a different order.

The ordering failure in

src/sage/dynamics/arithmetic_dynamics/projective_ds.py

is dealt here:

https://trac.sagemath.org/ticket/32817 (currently needs review)

Emmanuel Charpentier

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Nov 5, 2021, 8:30:26 AM11/5/21

to sage-release

FWIW, on another machine running Debian testing on core i5 + 8 GB RAM, upgrading from 9.5.beta2 to 9.5.beta5 succeeded, but ptestlong left 6 permanent failures, all of which being numerical noise or cosmetic booboos :

Test	Result	P/T	Comment
src/sage/functions/other.py	1 doctest failed	P	Numerical noise
src/sage/calculus/calculus.py	1 doctest failed	P	Cosmetic
src/sage/rings/complex_arb.pyx	11 doctests failed	P	Numerical noise
src/sage/functions/gamma.py	3 doctests failed	P	Numerical noise
src/sage/lfunctions/pari.py	1 doctest failed	P	Cosmetic
src/sage/rings/real_arb.pyx	6 doctests failed	P	Numerical noise

Re-running the failed tests gave the following results :

Running doctests with ID 2021-11-05-13-11-59-6a0701ff.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/functions/other.py
**********************************************************************
File "src/sage/functions/other.py", line 1581, in sage.functions.other.Function_factorial.__init__
Failed example:
    factorial(RBF(4.2))
Expected:
    [32.5780960503313 +/- 6.72e-14]
Got:
    [32.5780960503314 +/- 6.06e-14]
**********************************************************************
1 item had failures:
   1 of  39 in sage.functions.other.Function_factorial.__init__
    [501 tests, 1 failure, 14.39 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/functions/other.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 14.5 seconds
    cpu time: 16.1 seconds
    cumulative wall time: 14.4 seconds
Pytest is not installed, skip checking tests that rely on it.
Running doctests with ID 2021-11-05-13-12-17-67da9e1a.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/calculus/calculus.py
**********************************************************************
File "src/sage/calculus/calculus.py", line 1289, in sage.calculus.calculus.limit
Failed example:
    limit(e^(-1/x), x=0, dir='left', algorithm='fricas')              # optional - fricas
Expected:
    +Infinity
Got:
    plusInfinity()
**********************************************************************
1 item had failures:
   1 of  72 in sage.calculus.calculus.limit
    [455 tests, 1 failure, 13.43 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/calculus/calculus.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 13.5 seconds
    cpu time: 12.2 seconds
    cumulative wall time: 13.4 seconds
Pytest is not installed, skip checking tests that rely on it.
Running doctests with ID 2021-11-05-13-12-35-b5ca33e7.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/rings/complex_arb.pyx
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 1043, in sage.rings.complex_arb.ComplexBallField.?
Failed example:
    CBF.integral(lambda x, _: x.gamma(), 1 - CBF(i), 1 + CBF(i))
Expected:
    [+/- 4...e-15] + [1.5723926694981 +/- 4...e-14]*I
Got:
    [+/- 1.39e-15] + [1.57239266949806 +/- 8.33e-15]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 1147, in sage.rings.complex_arb.ComplexBallField.?
Failed example:
    CBF.integral(lambda x, _: (1 + i*x).gamma(), -1, 1)
Expected:
    [1.5723926694981 +/- 4...e-14] + [+/- 4...e-15]*I
Got:
    [1.57239266949806 +/- 8.33e-15] + [+/- 1.39e-15]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 2979, in sage.rings.complex_arb.ComplexBall.rising_factorial
Failed example:
    CBF(1/2).rising_factorial(CBF(2,3))
Expected:
    [-0.123060451458124 +/- ...e-16] + [0.040641263167655 +/- ...e-16]*I
Got:
    [-0.123060451458124 +/- 3.06e-16] + [0.0406412631676552 +/- 7.57e-17]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3491, in sage.rings.complex_arb.ComplexBall.gamma
Failed example:
    CBF(1, 1).gamma()
Expected:
    [0.498015668118356 +/- ...e-16] + [-0.154949828301811 +/- ...e-16]*I
Got:
    [0.498015668118356 +/- 1.26e-16] + [-0.1549498283018107 +/- 8.43e-17]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3495, in sage.rings.complex_arb.ComplexBall.gamma
Failed example:
    CBF(1, 1).gamma(0)
Expected:
    [0.498015668118356 +/- ...e-16] + [-0.154949828301811 +/- ...e-16]*I
Got:
    [0.498015668118356 +/- 1.26e-16] + [-0.1549498283018107 +/- 8.43e-17]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3499, in sage.rings.complex_arb.ComplexBall.gamma
Failed example:
    CBF(1, 1).gamma(CLF(i))
Expected:
    [0.32886684193500 +/- ...e-15] + [-0.18974945045621 +/- ...e-15]*I
Got:
    [0.328866841935004 +/- 7.07e-16] + [-0.189749450456210 +/- 9.05e-16]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3538, in sage.rings.complex_arb.ComplexBall.log_gamma
Failed example:
    CBF(-1).log_gamma()
Expected:
    nan + [-3.141592653589793 +/- ...e-16]*I
Got:
    nan + nan*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3540, in sage.rings.complex_arb.ComplexBall.log_gamma
Failed example:
    CBF(-3/2).log_gamma()
Expected:
    [0.860047015376481 +/- ...e-16] + [-6.28318530717959 +/- ...e-15]*I
Got:
    [0.860047015376481 +/- 3.82e-16] + [-6.283185307179586 +/- 6.77e-16]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3825, in sage.rings.complex_arb.ComplexBall.hypergeometric
Failed example:
    CBF(2+3*I).hypergeometric([1/4,1/3],[1/2])
Expected:
    [0.7871684267473 +/- 7...e-14] + [0.2749254173721 +/- 9...e-14]*I
Got:
    [0.7871684267473 +/- 6.79e-14] + [0.2749254173721 +/- 8.82e-14]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 3835, in sage.rings.complex_arb.ComplexBall.hypergeometric
Failed example:
    CBF(2016).hypergeometric([], [2/3])
Expected:
    [2.025642692328e+38 +/- ...e+25]
Got:
    [2.0256426923278e+38 +/- 9.59e+24]
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4930, in sage.rings.complex_arb.ComplexBall.laguerre_L
Failed example:
    CBF(5,7).laguerre_L(CBF(2,3), CBF(1,-2))
Expected:
    [5515.315030271 +/- ...e-10] + [-12386.942845271 +/- ...e-10]*I
Got:
    [5515.3150302713 +/- 5.02e-11] + [-12386.9428452714 +/- 6.21e-11]*I
**********************************************************************
6 items had failures:
   3 of   6 in sage.rings.complex_arb.ComplexBall.gamma
   2 of  17 in sage.rings.complex_arb.ComplexBall.hypergeometric
   1 of   4 in sage.rings.complex_arb.ComplexBall.laguerre_L
   2 of   6 in sage.rings.complex_arb.ComplexBall.log_gamma
   1 of   7 in sage.rings.complex_arb.ComplexBall.rising_factorial
   2 of  57 in sage.rings.complex_arb.ComplexBallField.?
    [644 tests, 11 failures, 4.38 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/rings/complex_arb.pyx  # 11 doctests failed
----------------------------------------------------------------------
Total time for all tests: 4.6 seconds
    cpu time: 4.5 seconds
    cumulative wall time: 4.4 seconds
Pytest is not installed, skip checking tests that rely on it.
Running doctests with ID 2021-11-05-13-12-43-59f88657.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/functions/gamma.py
**********************************************************************
File "src/sage/functions/gamma.py", line 360, in sage.functions.gamma.Function_gamma_inc._method_arguments
Failed example:
    gamma(b)
Expected:
    [1.00000000 +/- 8.07e-10]
Got:
    [1.0000000000 +/- 5.78e-11]
**********************************************************************
File "src/sage/functions/gamma.py", line 362, in sage.functions.gamma.Function_gamma_inc._method_arguments
Failed example:
    gamma(CBF(b))
Expected:
    [1.00000000 +/- 8.07e-10]
Got:
    [1.0000000000 +/- 5.78e-11]
**********************************************************************
File "src/sage/functions/gamma.py", line 364, in sage.functions.gamma.Function_gamma_inc._method_arguments
Failed example:
    gamma(CBF(b), 4)
Expected:
    [0.01831564 +/- 2.65e-9]
Got:
    [0.018315639 +/- 9.00e-10]
**********************************************************************
1 item had failures:
   3 of   6 in sage.functions.gamma.Function_gamma_inc._method_arguments
    [218 tests, 3 failures, 3.09 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/functions/gamma.py  # 3 doctests failed
----------------------------------------------------------------------
Total time for all tests: 3.2 seconds
    cpu time: 1.8 seconds
    cumulative wall time: 3.1 seconds
Pytest is not installed, skip checking tests that rely on it.
Running doctests with ID 2021-11-05-13-12-49-2129e1d9.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/lfunctions/pari.py
**********************************************************************
File "src/sage/lfunctions/pari.py", line 318, in sage.lfunctions.pari.lfun_number_field
Failed example:
    L(0)
Expected:
    0.000000000000000
Got:
      ***   Warning: normalizing a series with 0 leading term.
    0.000000000000000
**********************************************************************
1 item had failures:
   1 of   8 in sage.lfunctions.pari.lfun_number_field
    [166 tests, 1 failure, 0.95 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/lfunctions/pari.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 5.9 seconds
    cpu time: 0.8 seconds
    cumulative wall time: 0.9 seconds
Pytest is not installed, skip checking tests that rely on it.
Running doctests with ID 2021-11-05-13-12-59-df0ee8d0.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_packages,libsemigroups,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/rings/real_arb.pyx
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 755, in sage.rings.real_arb.RealBallField.euler_constant
Failed example:
    RBF.euler_constant()
Expected:
    [0.577215664901533 +/- ...e-16]
Got:
    [0.5772156649015329 +/- 9.00e-17]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 899, in sage.rings.real_arb.RealBallField.gamma
Failed example:
    RBF.gamma(RLF(pi))
Expected:
    [2.2880377953400 +/- ...e-14]
Got:
    [2.28803779534003 +/- 4.12e-15]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 1159, in sage.rings.real_arb.RealBall
Failed example:
    b
Expected:
    [-0.577215664901533 +/- ...e-16]
Got:
    [-0.5772156649015329 +/- 4.84e-17]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 1305, in sage.rings.real_arb.RealBall.__init__
Failed example:
    RealBall(RBF, sage.symbolic.constants.EulerGamma())
Expected:
    [0.577215664901533 +/- ...e-16]
Got:
    [0.5772156649015329 +/- 9.00e-17]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 3539, in sage.rings.real_arb.RealBall.rising_factorial
Failed example:
    RBF(1/2).rising_factorial(1/3)
Expected:
    [0.63684988431797 +/- ...e-15]
Got:
    [0.636849884317974 +/- 8.98e-16]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 3555, in sage.rings.real_arb.RealBall.psi
Failed example:
    RBF(1).psi()
Expected:
    [-0.577215664901533 +/- ...e-16]
Got:
    [-0.5772156649015329 +/- 4.84e-17]
**********************************************************************
6 items had failures:
   1 of   5 in sage.rings.real_arb.RealBall
   1 of  48 in sage.rings.real_arb.RealBall.__init__
   1 of   2 in sage.rings.real_arb.RealBall.psi
   1 of   3 in sage.rings.real_arb.RealBall.rising_factorial
   1 of   3 in sage.rings.real_arb.RealBallField.euler_constant
   1 of   6 in sage.rings.real_arb.RealBallField.gamma
    [544 tests, 6 failures, 0.41 s]
----------------------------------------------------------------------
sage -t --long --warn-long 71.2 --random-seed=0 src/sage/rings/real_arb.pyx  # 6 doctests failed
----------------------------------------------------------------------
Total time for all tests: 0.5 seconds
    cpu time: 0.4 seconds
    cumulative wall time: 0.4 seconds
Pytest is not installed, skip checking tests that rely on it.

axio...@yahoo.de

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Nov 30, 2021, 9:57:18 AM11/30/21

to sage-release

fixes for the fricas and findstat failures (fff) are now available on https://trac.sagemath.org/ticket/32886 and https://trac.sagemath.org/ticket/32694, in need of (very easy) review.

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